Merge pull request #5 from nearinj/master

Returns the ggplot2 objects in the function maaslin_plot_results
biobakery · Dec 2, 2024 · accf620 · accf620
2 parents 06e16f4 + ea1bbac
commit accf620
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Showing 4 changed files with 21 additions and 15 deletions.
diff --git a/R/maaslin3.R b/R/maaslin3.R
@@ -2326,6 +2326,7 @@ maaslin_plot_results <- function(output,
                                 plot_associations = TRUE,
                                 max_pngs = 30,
                                 balanced = FALSE) {
+    ret_plots <- list()
     # create an output folder and figures folder if it does not exist
     if (!file.exists(output)) {
         logging::loginfo("Creating output folder")
@@ -2363,7 +2364,7 @@ maaslin_plot_results <- function(output,
             heatmap_vars <- trimws(unlist(strsplit(heatmap_vars, ',')))
         }
 
-        maaslin3_summary_plot(
+        summary_plot <- maaslin3_summary_plot(
             merged_results,
             summary_plot_file,
             figures_folder,
@@ -2375,6 +2376,7 @@ maaslin_plot_results <- function(output,
             median_comparison_prevalence = median_comparison_prevalence,
             balanced = balanced
         )
+        ret_plots[["summary_plot"]] <- summary_plot
     }
 
     # Individual association plots
@@ -2410,9 +2412,9 @@ maaslin_plot_results <- function(output,
                 invokeRestart("muffleWarning")
             })
         })
-
-        return(plots_out)
+        ret_plots[["assocation_plots"]] <- plots_out
     }
+    return(ret_plots)
 }
 
 maaslin_plot_results_from_output <- function(output,
@@ -2437,6 +2439,7 @@ maaslin_plot_results_from_output <- function(output,
                                             plot_associations = TRUE,
                                             max_pngs = 30,
                                             balanced = FALSE) {
+    ret_plots <- list()
 
     # create an output folder and figures folder if it does not exist
     if (!file.exists(output)) {
@@ -2480,7 +2483,7 @@ maaslin_plot_results_from_output <- function(output,
             heatmap_vars <- trimws(unlist(strsplit(heatmap_vars, ',')))
         }
 
-        maaslin3_summary_plot(
+        summary_plot <- maaslin3_summary_plot(
             merged_results,
             summary_plot_file,
             figures_folder,
@@ -2492,6 +2495,7 @@ maaslin_plot_results_from_output <- function(output,
             median_comparison_prevalence = median_comparison_prevalence,
             balanced = balanced
         )
+        ret_plots[["summary_plot"]] <- summary_plot
     }
 
     # Individual associations
@@ -2567,17 +2571,14 @@ maaslin_plot_results_from_output <- function(output,
                 invokeRestart("muffleWarning")
             })
         })
-
-
-    } else {
-        plots_out <- NULL
+        ret_plots[["assocation_plots"]] <- plots_out
     }
 
     if ('logging::writeToFile' %in% names(logging::getLogger()[['handlers']])) {
         logging::removeHandler('logging::writeToFile')
     }
 
-    return(plots_out)
+    return(ret_plots)
 }
 
 ##########################################################

diff --git a/R/viz.R b/R/viz.R
@@ -473,6 +473,7 @@ maaslin3_summary_plot <-
             median_comparison_abundance = FALSE,
             median_comparison_prevalence = FALSE,
             balanced=FALSE) {
+        ret_plots <- list()
         if (first_n > 200) {
             logging::logerror(
                 paste(
@@ -686,6 +687,9 @@ maaslin3_summary_plot <-
         } else {
             final_plot <- NULL
         }
+        ret_plots[["coefficient"]] <- p1
+        ret_plots[["heat"]] <- p2
+        ret_plots[["final"]] <- final_plot
 
         # Save plot
         if (!is.null(final_plot)) {
@@ -736,6 +740,7 @@ maaslin3_summary_plot <-
                                  "summary_plot_gg.RDS",
                                  sep = ""))
         }
+        return(ret_plots)
     }
 
 # Create a scatterplot for abundance vs. continuous associations

diff --git a/tests/testthat/test_maaslin_plot_results.R b/tests/testthat/test_maaslin_plot_results.R
@@ -38,7 +38,7 @@ plot_out <- maaslin_plot_results(output = output_tmp,
                      median_comparison_abundance = FALSE,
                      max_significance = 0.1)
 
-expect_is(plot_out$var1$a$logistic, 'ggplot')
+expect_is(plot_out$assocation_plots$var1$a$logistic, 'ggplot')
 
 expect_equal(list.files(file.path(output_tmp, 'figures', 
                                   'association_plots', 'var1', 'logistic')),

diff --git a/tests/testthat/test_maaslin_plot_results_from_output.R b/tests/testthat/test_maaslin_plot_results_from_output.R
@@ -65,11 +65,11 @@ plot_out2 <- maaslin_plot_results(output = output_tmp,
                                  median_comparison_abundance = FALSE,
                                  max_significance = 0.1)
 
-expect_equal(plot_out$var1$a$logistic$data, plot_out2$var1$a$logistic$data)
-expect_equal(plot_out$var1$a$logistic$mapping, 
-             plot_out2$var1$a$logistic$mapping)
-expect_equal(plot_out$var1$a$logistic$scales, 
-             plot_out2$var1$a$logistic$scales)
+expect_equal(plot_out$assocation_plots$var1$a$logistic$data, plot_out2$assocation_plots$var1$a$logistic$data)
+expect_equal(plot_out$assocation_plots$var1$a$logistic$mapping, 
+             plot_out$assocation_plots2$var1$a$logistic$mapping)
+expect_equal(plot_out$assocation_plots$var1$a$logistic$scales, 
+             plot_out2$assocation_plots$var1$a$logistic$scales)
 
 unlink(output_tmp, recursive = T)